Hi, All! I have a question about the usage of the bedtools fisher tool. I have posted elsewhere but have not received answers.
I am trying to determine the significance of ChIP-seq peak overlap. I have two files with peaks all 101 bp in width. I entered the following command:
The file mm10.chrom.sizes contains each mouse chromosome and it's length. The output I received is:
This doesn't make sense to me. I feel that I am likely using the incorrect genome file, but am not sure what to use. Any advice?
I am trying to determine the significance of ChIP-seq peak overlap. I have two files with peaks all 101 bp in width. I entered the following command:
Code:
bedtools fisher -a Factor1.bed -b Factor2.bed -g mm10.chrom.sizes
Code:
# Number of query intervals: 27176 # Number of db intervals: 44018 # Number of overlaps: 25704 # Number of possible intervals (estimated): 13386626 # phyper(25704 - 1, 27176, 13386626 - 27176, 44018, lower.tail=F) # Contingency Table Of Counts #_________________________________________ # | in -b | not in -b | # in -a | 25704 | 1472 | # not in -a | 18314 | 13341136 | #_________________________________________ # p-values for fisher's exact test left right two-tail ratio 1 0 0 12720.451